Main
David Zhang
Experienced bioinformatician who enjoys learning and applying the best practices for method development. I focus on developing robust, user-friendly tools that harness transcriptomic data to improve the rate of genetic diagnosis.
Education
PhD, Bioinformatics
University College London
London, UK
Present - 2017
- Thesis: Using transcriptomics to improve the genetic diagnosis rate of rare disease patients.
MSc, Neuroscience
University College London
London, UK
2016 - 2015
- Thesis: The role of mitochondrial dysfunction in Xerodoma pigmentosum
- Grade: Merit (68%)
- Awarded post-graduate support scheme bursary (£10,000)
BSc, Biomedical science
University College London
London, UK
2015 - 2012
- Thesis: Investigating the function of CYFIP1 in the development of rat hippocampal neurons.
- Grade: 2:1 (69%)
H.S.
Queen Elizabeth’s School
Barnet, UK
2012 - 2007
- Grades: Maths (A*), Biology (A*), Chemistry (A*), Sociology (A).
Work Experience
Bioinformatician internship (2 months)
Remote, US
2021
- Goal: Set up an aberrant splicing detection pipeline for drug target discovery in C9orf72 ALS patients.
- Used docker to setup a reproducible workflow for running aberrant splicing analyses on an AWS instance.
Software & programming
Bioconductor packages
N/A
N/A
Present - 2020
- dasper: Detection of aberrant splicing events in RNA-sequencing. Author and maintainer.
- megadepth: BigWig and BAM related utilities. An R wrapper for the megadepth software developed by Chris Wilks. Co-author and maintainer.
- ODER: Optimising the definition of Expressed Regions. Submitted to Bioconductor. Co-author.
Web scraping
N/A
N/A
2021
- Applied the python packages Beautiful Soup and Selenium to web scrape information on all UK biotechnology companies.
Teaching Experience
Developing Bioconductor packages
University College London
Virtual Event
2020
Unit testing using testthat edition 3
rstats club
Virtual Event
2020
- Talk regarding unit testing fundamentals, the importance of testing and new features released in the R package testthat edition 3.
R fundamentals
Clinician Coders
London, UK
2020 - 2018
- Developed materials and lead workshops that aimed to teach R fundamentals to clinicians.
Selected Publications
Developmental Consequences of Defective ATG7-Mediated Autophagy in Humans
The New England Journal of Medicine
N/A
2021
- Collier J, Guissart C, Oláhová M, Sasorith S, Piron-Prunier F, Suom Fi, Zhang D, Martinez-Lopez N, Leboucq N, Bahr A, Azzarello-Burri S, Reich S, Schöls L, Polvikoski TM, Meyer P, Larrieu L, Schaefer AM, Alsaif HS, Alyamani S, Zuchner S, Barbosa IA, Deshpande C, Pyle A, Rauch A, Synofzik M, Alkuraya FS, Rivier F, Ryten M, McFarland R, Delahodde A, McWilliams TG, Koenig M, and Taylor RW.
- Role: Analyst
- DOI: https://doi.org/10.1056/NEJMoa1915722
Megadepth: efficient coverage quantification for BigWigs and BAMs
Bioinformatics
N/A
2021
- Wilks C, Ahmed O, Baker DN, Zhang D, Collado-Torres L, Langmead B.
- Role: R package developer.
- DOI: https://doi.org/10.1093/bioinformatics/btab152
Integration of eQTL and Parkinson’s disease GWAS data implicates 11 disease genes
Jama Neurology
N/A
2021
- Kia DA, Zhang D, Guelfi S, Manzoni C, Hubbard L, United Kingdom Brain Expression Consortium (UKBEC), International Parkinson’s Disease Genomics Consortium (IPDGC), Reynolds RH, Botía JA, Ryten M, Ferrari R, Lewis PA, Williams N, Trabzuni D, Hardy J, Wood NW.
- Role: Co-first author.
- DOI: https://doi.org/10.1001/jamaneurol.2020.5257
Incomplete annotation of disease-associated genes is limiting our understanding of Mendelian and complex neurogenetic disorders.
Science advances
N/A
2020
- Zhang D, Guelfi S, Ruiz SG, Costa B, Reynolds RH, D’Sa K, Liu W, Courtin T, Peterson A, Jaffe AE, Hardy J, Botia JA, Collado-Torres L and Ryten M.
- Role: First Author.
- DOI: https://doi.org/10.1126/sciadv.aay8299